hi, I want to use Cuffcompare to compare my assembled transcripts to a
reference annotation. My assembled transcripts is a Fasta format
produced by trinity, but Cuffcompare requried GTF file , so what
should I do? Thank you!
weimin zhao

Weimin Zhao,
It's not possible to use Trinity output directly with Cuffcompare.
You'll need to map your Trinity transcripts back to your reference
genome using something like Blat or Lastz, convert the mapped
transcripts to GTF format, and then run Cuffcompare.
You can run Lastz in Galaxy, but it's not clear to me how to convert
Lastz's output to GTF format, especially the format required by
Cuffcompare. You might try emailing the Cufflinks' authors directly or
the Trinity mailing list for some ideas.
Good luck,
J.